DNA-binding factor CTCF and long-range gene interactions in V(D)J recombination and oncogene activation

Almeida, Claudia Ribeiro de; Stadhouders, Ralph; Thongjuea, Supat; Soler, Éric; Hendriks, Rudolf W.

doi:10.1182/blood-2012-03-402586

Cited by 30 publications

(23 citation statements)

References 94 publications

(137 reference statements)

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“…Ctcf has been identified as an important regulator of longrange chromatin interactions in lymphocytes, 4 and viruses, and for removing apoptotic cells or cellular debris.…”

Section: Discussionmentioning

confidence: 99%

“…Parenchymal cells were removed by low-speed centrifugation at 300 r.p.m. for 3 min, and erythrocytes were lysed with 0.8% NH 4 Cl. Remaining liver cells were resuspended in culture medium.…”

Section: Preparation Of Single Cell Suspensionsmentioning

confidence: 99%

“…3,4 Moreover, Ctcf is important in a variety of regulatory functions, including genomic imprinting, X-chromosome inactivation and long-range chromatin interactions, hormone-responsive gene silencing, enhancer blocking and/or barrier gene insulation and transcriptional activation or repression. 3,4 The distinct functions of Ctcf are exerted by combinatorial use of 11-zinc fingers allowing it to bind highly divergent sequences. 3 Ctcf regulates chromatin architecture together with cohesion proteins, which are enriched at Ctcf-binding sites.…”

Section: Introductionmentioning

confidence: 99%

“…3,4 Ctcf is a highly conserved 11-zinc finger protein involved in the regulation of gene expression in a cell type-specific manner at complex gene clusters, such as the b-globin, major histocompatibility complex (MHC) class and the Ig gene loci. 3,4 Moreover, Ctcf is important in a variety of regulatory functions, including genomic imprinting, X-chromosome inactivation and long-range chromatin interactions, hormone-responsive gene silencing, enhancer blocking and/or barrier gene insulation and transcriptional activation or repression. 3,4 The distinct functions of Ctcf are exerted by combinatorial use of 11-zinc fingers allowing it to bind highly divergent sequences.…”

Section: Introductionmentioning

confidence: 99%

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The DNA-binding factor Ctcf critically controls gene expression in macrophages

et al. 2013

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“…Ctcf has been identified as an important regulator of longrange chromatin interactions in lymphocytes, 4 and viruses, and for removing apoptotic cells or cellular debris.…”

Section: Discussionmentioning

confidence: 99%

Section: Preparation Of Single Cell Suspensionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The DNA-binding factor Ctcf critically controls gene expression in macrophages

et al. 2013

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“…It is worth noting that CTCF is also well known for its enhancerblocking function and, as such, can limit the range of activity of nearby enhancers. 25,29 Within the immunoglobulin к light chain locus (Igк), conditional inactivation of the Ctcf gene in pre-B cells results in increased usage of the proximal Vк-3 gene family, which is rarely used in normal B cells. Increased Vк-3 genes usage correlates with increased interaction between the Igк locus enhancers and the Vк-3 genes in the absence of CTCF, suggesting that CTCF drives the specificity of enhancer-genes contacts at the Igк locus.…”

Section: Chromatin Loop Formation and Maintenancementioning

confidence: 99%

Transcription regulation by distal enhancers

et al. 2012

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G enome-wide chromatin profiling efforts have shown that enhancers are often located at large distances from gene promoters within the non-coding genome. Whereas enhancers can stimulate transcription initiation by communicating with promoters via chromatin looping mechanisms, we propose that enhancers may also stimulate transcription elongation by physical interactions with intronic elements. We review here recent findings derived from the study of the hematopoietic system. IntroductionThe development of multicellular organisms relies upon the capacity of stem and progenitor cells to respond to their microenvironment and differentiate upon exposure to specific stimuli. This multi-step process involves complex epigenetic changes within regulatory transcriptional networks, which contribute to the timely activation and repression of key developmental genes. Transcription of mammalian genes relies on the presence of a variety of cis-DNA regulatory sequences such as promoters and enhancers. Whereas gene promoters can be relatively easy to identify (i.e., at the 5' end of transcriptional units), locating and characterizing enhancers is far more complicated. Transgenic experiments carried out over the last few decades have taught us important lessons about transcriptional enhancers and genomic organization. Attempts to express transgenes in animals, under the control of endogenous promoter sequences, often resulted in weak

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Unbiased Interrogation of 3D Genome Topology Using Chromosome Conformation Capture Coupled to High-Throughput Sequencing (4C-Seq)

Brouwer

Hout

IJcken

et al. 2016

Methods in Molecular Biology

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The development and widespread implementation of chromosome conformation capture (3C) technology has allowed unprecedented new insight into how chromosomes are folded in three-dimensional (3D) space. 3C and its derivatives have contributed tremendously to the now widely accepted view that genome topology plays an important role in many major cellular processes, at a chromosome-wide scale, but certainly also at the level of individual genetic loci. A particularly popular application of 3C technology is to study transcriptional regulation, allowing researchers to draw maps of gene regulatory connections beyond the linear genome through addition of the third dimension. In this chapter, we provide a highly detailed protocol describing 3C coupled to high-throughput sequencing (referred to as 3C-Seq or more commonly 4C-Seq), allowing the unbiased interrogation of genome-wide chromatin interactions with specific genomic regions of interest. Interactions between spatially clustered DNA fragments are revealed by crosslinking the cells with formaldehyde, digesting the genome with a restriction endonuclease and performing a proximity ligation step to link interacting genomic fragments. Next, interactions with a selected DNA fragment are extracted from the 3C library through a second round of digestion and ligation followed by an inverse PCR. The generated products are immediately compatible with high-throughput sequencing, and amplicons from different PCR reactions can easily be multiplexed to dramatically increase throughput. Finally, we provide suggestions for data analysis and visualization.

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DNA-binding factor CTCF and long-range gene interactions in V(D)J recombination and oncogene activation

Cited by 30 publications

References 94 publications

The DNA-binding factor Ctcf critically controls gene expression in macrophages

The DNA-binding factor Ctcf critically controls gene expression in macrophages

Transcription regulation by distal enhancers

Unbiased Interrogation of 3D Genome Topology Using Chromosome Conformation Capture Coupled to High-Throughput Sequencing (4C-Seq)

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